The latches Lone Ranger used are sash locks, great solution and should engage very smoothly. The good thing is that they are available at most hardware stores.
I like that the ones you choose are draw latches, but I am familiar with that style and they do tend to bind up a bit. Have you looked through the latches on the McmasterCarr site? Basically what you have would be a "turn-to-close draw latch" there are other industry options available that you might be happier with.
Low profile, secure holding, smooth operating latches are actually quite an issue to find.
I've also recently been putting a lot of work into into attachment methods for the side panels. The regular panels I make with the large doors are bolted into the OE holes.
I'm about to make the first set of non-operating side panel replacements though, and since they will just be plastic panels like on the tailgates I need to have captive fasteners since there will be no access to the reverse side. Went through and tested all manner of fasteners and found the best fit to be SouthCo's fast lead DZUS screws. They are a standard system on aircraft and basically it is similar to the little U clips and screws you see in automotive applications, but much larger and with speed threads for repeated easy removal. There are a boat-load of dimensional requirements between the screw and the clip and I have my run of them set up for 1/4" panel thickness since that is the size of the marine grade plastic, there are also minimum orders and you have to have an account....... but I could set you up with enough for side panels as long as the panel was 1/4" in thickness as well.
The nice thing about these is that the clip is captive to the body, and the screw is actually captive to the panel as well, so there are no loose parts.
Now your hinges, I think the exposed flap hinges actually look great on there, I might consider doing something like that on the side panels. I just intuitively used the same system as I have on the tailgate lids, but it is not necessary since loads are no slid over the side panel, great idea, and simpler to construct as well. It would probably not be as cost effective, but would certainly save fabrication time....
Thanks for the idea!